GeneBe

rs776920005

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4

The NM_000421.5(KRT10):​c.1654_1683delAGCTCCGGCGGCGGATACGGCGGCGGCAGC​(p.Ser552_Ser561del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000259 in 1,275,478 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.000026 ( 0 hom. )

Consequence

KRT10
NM_000421.5 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.15
Variant links:
Genes affected
KRT10 (HGNC:6413): (keratin 10) This gene encodes a member of the type I (acidic) cytokeratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. Mutations in this gene are associated with epidermolytic hyperkeratosis. This gene is located within a cluster of keratin family members on chromosome 17q21. [provided by RefSeq, Jul 2008]
KRT10-AS1 (HGNC:28305): (KRT10 antisense RNA 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM4
Nonframeshift variant in NON repetitive region in NM_000421.5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KRT10NM_000421.5 linkc.1654_1683delAGCTCCGGCGGCGGATACGGCGGCGGCAGC p.Ser552_Ser561del conservative_inframe_deletion Exon 7 of 8 ENST00000269576.6 NP_000412.4 P13645
KRT10NM_001379366.1 linkc.1654_1683delAGCTCCGGCGGCGGATACGGCGGCGGCAGC p.Ser552_Ser561del conservative_inframe_deletion Exon 7 of 8 NP_001366295.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRT10ENST00000269576.6 linkc.1654_1683delAGCTCCGGCGGCGGATACGGCGGCGGCAGC p.Ser552_Ser561del conservative_inframe_deletion Exon 7 of 8 1 NM_000421.5 ENSP00000269576.5 P13645

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.0000259
AC:
33
AN:
1275478
Hom.:
0
AF XY:
0.0000221
AC XY:
14
AN XY:
634488
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000322
Gnomad4 OTH exome
AF:
0.0000191
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-38975103; API